HIV-1 drug resistance seriously impacts treatment options for infected individuals. It is recommended that HIV-1 infection be treated with combination antiretroviral therapy containing at least two classes of drugs. A combination of 2 nucleoside analog reverse transcriptase (RT) inhibitors (NRTIs) and 1 nonnucleoside RT inhibitor (NNRTI) is commonly used. During treatment, HIV-1 can acquire mutations that allow escape from inhibition by antiretroviral drugs. Drug resistant viruses can be stable within the host for long periods of time and can be transmitted horizontally or vertically to new individuals. However, the sites of origin and persistence of drug resistance within individuals over time has not been studied in depth. We hypothesize that drug resistant viruses will emerge multifocally in tissues, such as mucosal sites, the central nervous system, and lymph nodes, before resistance is seen in blood and will persist for longer periods of time as compared to blood. We also propose that differences in the pharmacokinetics and pharmacodynamics of antiretrovirals in these anatomic compartments strongly influence the selection and persistence of drug resistance. Nonhuman primate models have been useful in studying AIDS pathogenesis and immunology, using simian immunodeficiency virus (SIV). Because NNRTIs do not inhibit SIV, these drugs cannot be studied in the SIV model. Therefore, we developed a macaque model to study HIV-1 drug resistance in vivo. This model uses macaques infected with a pathogenic chimeric virus consisting of SIVmne containing the HIV-1HxB2 RT coding region (RT-SHIVmne). In Specific Aim 1, we propose to longitudinally examine the emergence of drug- resistant RT-SHIVmne in the blood and in different anatomical compartments that arise during NRTI or NNRTI monotherapy. Because HIV-1 persists in cellular and tissue reservoirs even during suppressive antiretroviral therapy, we propose in Specific Aim 2 to determine the origin of the re-emergence of wild-type virus and persistence of drug-resistant virus after discontinuation of monotherapy and after initiation of antiretroviral therapy using a regimen of all new drugs or one that includes the drug used in monotherapy in the infected animals. To explore whether site-specific differences in the emergence of drug resistant viruses are explained by different site-specific drug concentrations, we propose in Specific Aim 3 to examine the pharmacokinetics and pharmacodynamics of the antiretrovirals in the blood and tissues during and after therapy. The proposed studies are difficult to execute in humans but can be readily performed in our RT-SHIVmne model of antiretroviral therapy and drug resistance. These experiments will provide new insights into the anatomic origin of drug resistance, its persistence on and off antiretroviral therapy, and the influence of site- specific variation in antiretroviral pharmacokinetics. This work should help determine better strategies for treating HIV-infected individuals, particularly those harboring and potentially transmitting drug resistant virus.